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Jacaerys was the eldest son of Rhaenyra Targaryen and her first husband/cousin, Laenor Velaryon. His mother was the first child and daughter of Viserys I Targaryen, who did not change the succession of the Iron Throne upon the birth of his sons. This therefore made Jacaerys second in line for the throne. When his grandfather died, his uncle was named Aegon II Targaryen, on the orders of his step-grandmother Alicent Hightower. When Rhaenyra heard the news, the Dance of the Dragons began. By this time, Laenor had presumably died and Jacaerys' mother had remarried her uncle Daemon Targaryen, and had two sons with him. In order to gain more supporters on the mainland of Westeros, Rhaenyra sent him on his dragon, Vermax, to recruit houses in the North and the Vale. House Arryn, the house of Jacaerys' grandmother Aemma Arryn, were persuaded to join the Blacks. He also persuaded the Starks of Winterfell, meaning that the Northern houses all followed his mother. After his grandmother Rhaenys died at the hands of his twouncles, Rhaenyra sent his younger brothers to Essos, however the youngest came back on his dying dragon. Although his mother forbade it, he went to claim his other brother from the enemy fleet on Vermax. However, the dragon dropped into the sea, where they were both shot numerous times, and where they were said to have soaked up more arrows than seawater.

Jacaerys was fifteen-years-old at the start of the civil war which became known as the Dance of the Dragons. He rode his dragon, Vermax, to the Eyrie, Sisterton, White Harbor, and Winterfell to raise support for his mother's claim. After successfully gaining the Vale of Arryn for the blacks, he also gained the North through the Pact of Ice and Fire.

Jacaerys took part in the battle of the Gullet where Vermax flew too low and went crashing into the sea. It was said that Jace leapt free and clung to a piece of smoking wreckage for a few heartbeats until some crossbowmen on the nearest Myrishship began loosing quarrels at him. The prince was struck once, and then again. Finally, one quarrel took him in the neck and he was swallowed by the sea.